Search Results - "FRANCIS, Joshua M"

Chromothripsis from DNA damage in micronuclei by Zhang, Cheng-Zhong, Spektor, Alexander, Cornils, Hauke, Francis, Joshua M., Jackson, Emily K., Liu, Shiwei, Meyerson, Matthew, Pellman, David

“…Genome sequencing has uncovered a new mutational phenomenon in cancer and congenital disorders called chromothripsis. Chromothripsis is characterized by…”
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Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers by Zhang, Xiaoyang, Choi, Peter S, Francis, Joshua M, Imielinski, Marcin, Watanabe, Hideo, Cherniack, Andrew D, Meyerson, Matthew

“…Matthew Meyerson and colleagues identify focal amplifications of regions harboring super-enhancers near KLF5 , USP12 , PARD6B and MYC in epithelial cancers…”
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Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients by van de Wetering, Marc, Francies, Hayley E., Francis, Joshua M., Bounova, Gergana, Iorio, Francesco, Pronk, Apollo, van Houdt, Winan, van Gorp, Joost, Taylor-Weiner, Amaro, Kester, Lennart, McLaren-Douglas, Anne, Blokker, Joyce, Jaksani, Sridevi, Bartfeld, Sina, Volckman, Richard, van Sluis, Peter, Li, Vivian S.W., Seepo, Sara, Sekhar Pedamallu, Chandra, Cibulskis, Kristian, Carter, Scott L., McKenna, Aaron, Lawrence, Michael S., Lichtenstein, Lee, Stewart, Chip, Koster, Jan, Versteeg, Rogier, van Oudenaarden, Alexander, Saez-Rodriguez, Julio, Vries, Robert G.J., Getz, Gad, Wessels, Lodewyk, Stratton, Michael R., McDermott, Ultan, Meyerson, Matthew, Garnett, Mathew J., Clevers, Hans

“…In Rspondin-based 3D cultures, Lgr5 stem cells from multiple organs form ever-expanding epithelial organoids that retain their tissue identity. We report the…”
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Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma by Tirosh, Itay, Venteicher, Andrew S., Hebert, Christine, Escalante, Leah E., Patel, Anoop P., Yizhak, Keren, Fisher, Jonathan M., Rodman, Christopher, Mount, Christopher, Filbin, Mariella G., Neftel, Cyril, Desai, Niyati, Nyman, Jackson, Izar, Benjamin, Luo, Christina C., Francis, Joshua M., Patel, Aanand A., Onozato, Maristela L., Riggi, Nicolo, Livak, Kenneth J., Gennert, Dave, Satija, Rahul, Nahed, Brian V., Curry, William T., Martuza, Robert L., Mylvaganam, Ravindra, Iafrate, A. John, Frosch, Matthew P., Golub, Todd R., Rivera, Miguel N., Getz, Gad, Rozenblatt-Rosen, Orit, Cahill, Daniel P., Monje, Michelle, Bernstein, Bradley E., Louis, David N., Regev, Aviv, Suvà, Mario L.

“…A single sentence summarizing your paper (websum), which will appear online on the table of contents and in e-alerts, has been provided below. Please check…”
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Small-molecule targeting of brachyury transcription factor addiction in chordoma by Sharifnia, Tanaz, Wawer, Mathias J., Chen, Ting, Huang, Qing-Yuan, Weir, Barbara A., Sizemore, Ann, Lawlor, Matthew A., Goodale, Amy, Cowley, Glenn S., Vazquez, Francisca, Ott, Christopher J., Francis, Joshua M., Sassi, Slim, Cogswell, Patricia, Sheppard, Hadley E., Zhang, Tinghu, Gray, Nathanael S., Clarke, Paul A., Blagg, Julian, Workman, Paul, Sommer, Josh, Hornicek, Francis, Root, David E., Hahn, William C., Bradner, James E., Wong, Kwok K., Clemons, Paul A., Lin, Charles Y., Kotz, Joanne D., Schreiber, Stuart L.

“…Chordoma is a primary bone cancer with no approved therapy 1 . The identification of therapeutic targets in this disease has been challenging due to the…”
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EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing by Francis, Joshua M, Zhang, Cheng-Zhong, Maire, Cecile L, Jung, Joonil, Manzo, Veronica E, Adalsteinsson, Viktor A, Homer, Heather, Haidar, Sam, Blumenstiel, Brendan, Pedamallu, Chandra Sekhar, Ligon, Azra H, Love, J Christopher, Meyerson, Matthew, Ligon, Keith L

“…Glioblastomas (GBM) with EGFR amplification represent approximately 50% of newly diagnosed cases, and recent studies have revealed frequent coexistence of…”
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Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor by Zhang, Xiaoyang, Choi, Peter S, Francis, Joshua M, Gao, Galen F, Campbell, Joshua D, Ramachandran, Aruna, Mitsuishi, Yoichiro, Ha, Gavin, Shih, Juliann, Vazquez, Francisca, Tsherniak, Aviad, Taylor, Alison M, Zhou, Jin, Wu, Zhong, Berger, Ashton C, Giannakis, Marios, Hahn, William C, Cherniack, Andrew D, Meyerson, Matthew

“…The Krüppel-like family of transcription factors plays critical roles in human development and is associated with cancer pathogenesis. Krüppel-like factor 5…”
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Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma by Llabata, Paula, Mitsuishi, Yoichiro, Choi, Peter S, Cai, Diana, Francis, Joshua M, Torres-Diz, Manuel, Udeshi, Namrata D, Golomb, Lior, Wu, Zhong, Zhou, Jin, Svinkina, Tanya, Aguilera-Jimenez, Estrella, Liu, Yanli, Carr, Steven A, Sanchez-Cespedes, Montse, Meyerson, Matthew, Zhang, Xiaoyang

“…Genomic analysis of lung adenocarcinomas has revealed that the gene, which encodes a heterodimeric partner of the MYC-interacting protein MAX, is significantly…”
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Dynamic epigenetic regulation by menin during pancreatic islet tumor formation by Lin, Wenchu, Watanabe, Hideo, Peng, Shouyong, Francis, Joshua M, Kaplan, Nathan, Pedamallu, Chandra Sekhar, Ramachandran, Aruna, Agoston, Agoston, Bass, Adam J, Meyerson, Matthew

“…The tumor suppressor gene MEN1 is frequently mutated in sporadic pancreatic neuroendocrine tumors (PanNET) and is responsible for the familial multiple…”
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Utilizing feline oral squamous cell carcinoma patients to develop NQO1-targeted therapy by Lundberg, Alycen P., Boudreau, Matthew W., Selting, Kim A., Chatkewitz, Lindsay E., Samuelson, Jonathan, Francis, Joshua M., Parkinson, Elizabeth I., Barger, Anne M., Hergenrother, Paul J., Fan, Timothy M.

“…Developing effective therapies for the treatment of advanced head-and-neck squamous cell carcinoma (HNSCC) remains a major challenge, and there is a limited…”
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tumor suppressor Cdc73 functionally associates with CPSF and CstF 3' mRNA processing factors by Rozenblatt-Rosen, Orit, Nagaike, Takashi, Francis, Joshua M, Kaneko, Syuzo, Glatt, Karen A, Hughes, Christina M, LaFramboise, Thomas, Manley, James L, Meyerson, Matthew

“…The CDC73 tumor suppressor gene is mutationally inactivated in hereditary and sporadic parathyroid tumors. Its product, the Cdc73 protein, is a component of…”
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Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target by Watanabe, Hideo, Francis, Joshua M, Woo, Michele S, Etemad, Banafsheh, Lin, Wenchu, Fries, Daniel F, Peng, Shouyong, Snyder, Eric L, Tata, Purushothama Rao, Izzo, Francesca, Schinzel, Anna C, Cho, Jeonghee, Hammerman, Peter S, Verhaak, Roel G, Hahn, William C, Rajagopal, Jayaraj, Jacks, Tyler, Meyerson, Matthew

“…The NKX2-1 transcription factor, a regulator of normal lung development, is the most significantly amplified gene in human lung adenocarcinoma. To study the…”
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ARID1A and TERT promoter mutations in dedifferentiated meningioma by Abedalthagafi, Malak S, Bi, Wenya Linda, Merrill, Parker H, Gibson, William J, Rose, Matthew F, Du, Ziming, Francis, Joshua M, Du, Rose, Dunn, Ian F, Ligon, Azra H, Beroukhim, Rameen, Santagata, Sandro

“…Unlike patients with World Health Organization (WHO) grade I meningiomas, which are considered benign, patients with WHO grade III meningiomas have very high…”
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Constitutive asymmetric dimerization drives oncogenic activation of epidermal growth factor receptor carboxyl-terminal deletion mutants by Park, Angela K J, Francis, Joshua M, Park, Woong-Yang, Park, Joon-Oh, Cho, Jeonghee

“…Genomic alterations targeting the Epidermal Growth Factor Receptor (EGFR) gene have been strongly associated with cancer pathogenesis. The clinical…”
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Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors by Adalsteinsson, Viktor A., Ha, Gavin, Freeman, Samuel S., Choudhury, Atish D., Stover, Daniel G., Parsons, Heather A., Gydush, Gregory, Reed, Sarah C., Rotem, Denisse, Rhoades, Justin, Loginov, Denis, Livitz, Dimitri, Rosebrock, Daniel, Leshchiner, Ignaty, Kim, Jaegil, Stewart, Chip, Rosenberg, Mara, Francis, Joshua M., Zhang, Cheng-Zhong, Cohen, Ofir, Oh, Coyin, Ding, Huiming, Polak, Paz, Lloyd, Max, Mahmud, Sairah, Helvie, Karla, Merrill, Margaret S., Santiago, Rebecca A., O’Connor, Edward P., Jeong, Seong H., Leeson, Rachel, Barry, Rachel M., Kramkowski, Joseph F., Zhang, Zhenwei, Polacek, Laura, Lohr, Jens G., Schleicher, Molly, Lipscomb, Emily, Saltzman, Andrea, Oliver, Nelly M., Marini, Lori, Waks, Adrienne G., Harshman, Lauren C., Tolaney, Sara M., Van Allen, Eliezer M., Winer, Eric P., Lin, Nancy U., Nakabayashi, Mari, Taplin, Mary-Ellen, Johannessen, Cory M., Garraway, Levi A., Golub, Todd R., Boehm, Jesse S., Wagle, Nikhil, Getz, Gad, Love, J. Christopher, Meyerson, Matthew

“…Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and…”
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Chromatin Looping Shapes KLF5-Dependent Transcriptional Programs in Human Epithelial Cancers by Liu, Yanli, Guo, Bingqian, Aguilera-Jimenez, Estrella, Chu, Vivian S, Zhou, Jin, Wu, Zhong, Francis, Joshua M, Yang, Xiaojun, Choi, Peter S, Bailey, Swneke D, Zhang, Xiaoyang

“…Activation of transcription factors is a key driver event in cancer. We and others have recently reported that the Krüppel-like transcription factor KLF5 is…”
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Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer by Lohr, Jens G, Adalsteinsson, Viktor A, Cibulskis, Kristian, Choudhury, Atish D, Rosenberg, Mara, Cruz-Gordillo, Peter, Francis, Joshua M, Zhang, Cheng-Zhong, Shalek, Alex K, Satija, Rahul, Trombetta, John J, Lu, Diana, Tallapragada, Naren, Tahirova, Narmin, Kim, Sora, Blumenstiel, Brendan, Sougnez, Carrie, Lowe, Alarice, Wong, Bang, Auclair, Daniel, Van Allen, Eliezer M, Nakabayashi, Mari, Lis, Rosina T, Lee, Gwo-Shu M, Li, Tiantian, Chabot, Matthew S, Ly, Amy, Taplin, Mary-Ellen, Clancy, Thomas E, Loda, Massimo, Regev, Aviv, Meyerson, Matthew, Hahn, William C, Kantoff, Philip W, Golub, Todd R, Getz, Gad, Boehm, Jesse S, Love, J Christopher

“…Whole-exome sequencing of circulating tumor cells enables accurate and powered calling of somatic point mutations. Comprehensive analyses of cancer genomes…”
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SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas by Watanabe, Hideo, Ma, Qiuping, Peng, Shouyong, Adelmant, Guillaume, Swain, Danielle, Song, Wenyu, Fox, Cameron, Francis, Joshua M, Pedamallu, Chandra Sekhar, DeLuca, David S, Brooks, Angela N, Wang, Su, Que, Jianwen, Rustgi, Anil K, Wong, Kwok-kin, Ligon, Keith L, Liu, X Shirley, Marto, Jarrod A, Meyerson, Matthew, Bass, Adam J

“…The transcription factor SOX2 is an essential regulator of pluripotent stem cells and promotes development and maintenance of squamous epithelia. We previously…”
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Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia by Wang, Lili, Fan, Jean, Francis, Joshua M, Georghiou, George, Hergert, Sarah, Li, Shuqiang, Gambe, Rutendo, Zhou, Chensheng W, Yang, Chunxiao, Xiao, Sheng, Cin, Paola Dal, Bowden, Michaela, Kotliar, Dylan, Shukla, Sachet A, Brown, Jennifer R, Neuberg, Donna, Alessi, Dario R, Zhang, Cheng-Zhong, Kharchenko, Peter V, Livak, Kenneth J, Wu, Catherine J

“…Intra-tumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In…”
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Cetuximab Response of Lung Cancer―Derived EGF Receptor Mutants Is Associated with Asymmetric Dimerization by JEONGHEE CHO, LIANG CHEN, GREULICH, Heidi, JOHNSON, Bruce E, ECK, Michael J, JÄNNE, Pasi A, WONG, Kwok-Kin, MEYERSON, Matthew, SANGJI, Naveen, OKABE, Takafumi, YONESAKA, Kimio, FRANCIS, Joshua M, FLAVIN, Richard J, JOHNSON, William, JIHYUN KWON, SOYOUNG YU

“…Kinase domain mutations of the EGF receptor (EGFR) are common oncogenic events in lung adenocarcinoma. Here, we explore the dependency upon asymmetric…”
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